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STEM CELL BIOLOGY

Molecular landscape of immune pressure and escape in aplastic anemia

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Abstract

Idiopathic aplastic anemia (IAA) pathophysiology is dominated by autoreactivity of human leukocyte antigen (HLA)-restricted T-cells against antigens presented by hematopoietic stem and progenitor cells (HSPCs). Expansion of PIGA and HLA class I mutant HSPCs have been linked to immune evasion from T-cell mediated pressures. We hypothesized that in analogy with antitumor immunity, the pathophysiological cascade of immune escape in IAA is initiated by immunoediting pressures and culminates with mechanisms of clonal evolution characterized by hits in immune recognition and response genes. To that end, we studied the genetic and transcriptomic make-up of the antigen presentation complexes in a large cohort of patients with IAA and paroxysmal nocturnal hemoglobinuria (PNH) by using single-cell RNA, high throughput DNA sequencing and single nucleotide polymorphism (SNP)-array platforms. At disease onset, HSPCs displayed activation of selected HLA class I and II-restricted mechanisms, without extensive inhibition of immune checkpoint apparatus. Using a newly implemented bioinformatic framework we found that not only class I but also class II genes were often impaired by acquisition of genetic aberrations. We also demonstrated the presence of novel somatic alterations in immune genes possibly contributing to the evasion from the autoimmune T-cells. In contrast, these hits were absent in myeloid neoplasia. These aberrations were not mutually exclusive with PNH and did not correlate with the accumulation of myeloid-driver hits. Our findings shed light on the mechanisms of immune activation and escape in IAA and define alternative modes of clonal hematopoiesis.

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Fig. 1: Study design.
Fig. 2: Single-cell RNAseq analysis of antigen presentation machinery genes in HSPCs in aplastic anemia patients and healthy controls.
Fig. 3: Landscape of HLA aberrations.
Fig. 4: Immune, PNH and myeloid landscape.

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Acknowledgements

This work was supported by US National Institute of Health (NIH) grants R35 HL135795, R01HL123904, R01 380HL118281, R01 HL128425, R01 HL132071, Edward P. Evans Foundation, The Leukemia & Lymphoma Society TRP Award 6645-22 (to JPM), Aplastic Anemia and MDS International Foundation, Italian Society of Hematology, Fondation ARC pour la Recherche sur le Cancer, Association HPN France – Aplasie medullaire and Foundation For Rare Diseases (FFRD) (to SP), VeloSano Pilot Award and Vera and Joseph Dresner Foundation–MDS (to VV), Edward P. Evans Foundation (to CG). The CIBMTR is supported primarily by Public Health Service U24CA076518 from the National Cancer Institute (NCI), the National Heart, Lung and Blood Institute (NHLBI) and the National Institute of Allergy and Infectious Diseases (NIAID); HHSH250201700006C from the Health Resources and Services Administration (HRSA); and N00014-20-1-2705 and N00014-20-1-2832 from the Office of Naval Research. We greatly thank Lucia D’Aprano, for her IT assistance in the development of the HLA mutational pipeline. We deeply thank all the reviewers who constructively contributed to improve this work.

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  1. These authors contributed equally: Simona Pagliuca, Carmelo Gurnari.

Authors and Affiliations

  1. Translational Hematology and Oncology Research Program, Cleveland Clinic, Cleveland, OH, USA

    Simona Pagliuca, Carmelo Gurnari, Laila Terkawi, Minako Mori, Valeria Visconte & Jaroslaw P. Maciejewski

  2. Department of Hematology, CHRU Nancy, Vandœuvre-lès-Nancy, France

    Simona Pagliuca

  3. Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy

    Carmelo Gurnari

  4. Novocraft Technologies Sdn Bhd, Kuala Lumpur, Malaysia

    Colin Hercus

  5. Inserm UMR_S1256 Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 54500, Vandœuvre-lès-Nancy, France

    Sébastien Hergalant

  6. Munich Leukemia Laboratory, MLL, Munich, Germany

    Niroshan Nadarajah, Adam Wahida & Torsten Haferlach

  7. Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD, USA

    Weiyin Zhou & Shahinaz M. Gadalla

  8. Cancer Genomics Research Laboratory, Frederick National Laboratory, Frederick, MD, USA

    Weiyin Zhou

  9. CIBMTR® (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA

    Stephen Spellman

  10. State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, No. 288 Nanjing Rd, Tianjin, China

    Caiying Zhu & Ping Zhu

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  1. Simona Pagliuca
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Contributions

SP designed the study, collected, analyzed and interpreted the data, developed the pipeline for the variant calling in HLA region, performed the bioinformatic and statistical analyses, and wrote the manuscript. CG performed NGS experiments, clinical and molecular data collection and participated in the analysis interpretation and critical manuscript revision. CH developed NovoHLA and the methodology for the calculation of copy number variation. SH helped in optimizing the bioanalytical HLA workflow and developing the associated bioinformatic pipeline. NN performed WGS experiments, AW, LT, MM helped in sample and data collection; SS and SG provided HLA and SNP array data for the TOAA/CIBMTR IAA cohort and gave helpful intellectual insights. WZ analyzed SNP-array data. VV helped in data collection and interpretation, gave important intellectual inputs, and edited the manuscript; CZ and PZ provided single-cell RNA samples and gave meaningful intellectual inputs for the deployed analytical methodology. TH supervised the genotyping experiments in MLL, helped in data interpretation and edited the manuscript; JPM designed and conceptualized the study, supervised genomic experiments, provided funding and resources, interpreted the data analysis and edited the manuscript.

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Correspondence to Jaroslaw P. Maciejewski.

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This research was conducted in absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Collaboration between Cleveland Clinic and Novocraft was based on a no-profit academic partnership.

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Pagliuca, S., Gurnari, C., Hercus, C. et al. Molecular landscape of immune pressure and escape in aplastic anemia. Leukemia 37, 202–211 (2023). https://doi.org/10.1038/s41375-022-01723-w

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